Solvation thermodynamic mapping of molecular surfaces in AmberTools: GIST.
J Comput Chem
; 37(21): 2029-37, 2016 08 05.
Article
in En
| MEDLINE
| ID: mdl-27317094
ABSTRACT
The expulsion of water from surfaces upon molecular recognition and nonspecific association makes a major contribution to the free energy changes of these processes. In order to facilitate the characterization of water structure and thermodynamics on surfaces, we have incorporated Grid Inhomogeneous Solvation Theory (GIST) into the CPPTRAJ toolset of AmberTools. GIST is a grid-based implementation of Inhomogeneous Fluid Solvation Theory, which analyzes the output from molecular dynamics simulations to map out solvation thermodynamic and structural properties on a high-resolution, three-dimensional grid. The CPPTRAJ implementation, called GIST-cpptraj, has a simple, easy-to-use command line interface, and is open source and freely distributed. We have also developed a set of open-source tools, called GISTPP, which facilitate the analysis of GIST output grids. Tutorials for both GIST-cpptraj and GISTPP can be found at ambermd.org. © 2016 Wiley Periodicals, Inc.
Key words
Full text:
1
Database:
MEDLINE
Main subject:
Thermodynamics
/
Water
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Proteins
/
Molecular Dynamics Simulation
Language:
En
Journal:
J Comput Chem
Journal subject:
QUIMICA
Year:
2016
Type:
Article